--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/gff/VcfToGff.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,149 @@
+package gff;
+
+import java.io.PrintStream;
+
+import fileIO.ByteFile;
+import fileIO.ByteStreamWriter;
+import fileIO.FileFormat;
+import shared.Parser;
+import shared.PreParser;
+import shared.ReadStats;
+import shared.Timer;
+import shared.Tools;
+import structures.ByteBuilder;
+import var2.VCFLine;
+
+/**
+ * Stripped out of GffLine into independent class.
+ * @author Brian Bushnell
+ * @date Sep 12, 2018
+ *
+ */
+public class VcfToGff {
+
+	/** Translates VCF to GFF */
+	public static void main(String[] args){
+		Timer t=new Timer();
+		PrintStream outstream=System.err;
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, new Object() { }.getClass().getEnclosingClass(), false);
+			args=pp.args;
+			outstream=pp.outstream;
+			t.outstream=outstream;
+		}
+		
+		Parser parser=new Parser();
+		String in=null;
+		String out=null;
+		boolean overwrite=true, append=false;
+		
+		//Parse each argument
+		for(int i=0; i<args.length; i++){
+			String arg=args[i];
+			
+			//Break arguments into their constituent parts, in the form of "a=b"
+			String[] split=arg.split("=");
+			String a=split[0].toLowerCase();
+			String b=split.length>1 ? split[1] : null;
+			
+			if(a.equals("in") || a.equals("vcf")){
+				in=b;
+			}else if(a.equals("out") || a.equals("gff")){
+				out=b;
+			}else if(parser.parse(arg, a, b)){
+				//do nothing
+			}else if(in==null && b==null && i==0 && Tools.canRead(arg)){
+				in=arg;
+			}else if(in==null && b==null && i==1){
+				out=arg;
+			}else{
+				outstream.println("Unknown parameter "+args[i]);
+				assert(false) : "Unknown parameter "+args[i];
+			}
+		}
+		
+		{//Process parser fields
+			overwrite=ReadStats.overwrite=parser.overwrite;
+			append=ReadStats.append=parser.append;
+		}
+		
+		//Ensure output files can be written
+		if(!Tools.testOutputFiles(overwrite, append, false, out)){
+			outstream.println((out==null)+", "+out);
+			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out+"\n");
+		}
+
+		//Ensure input files can be read
+		if(!Tools.testInputFiles(false, true, in)){
+			throw new RuntimeException("\nCan't read some input files.\n");  
+		}
+
+		//Ensure that no file was specified multiple times
+		if(!Tools.testForDuplicateFiles(true, in, out)){
+			throw new RuntimeException("\nSome file names were specified multiple times.\n");
+		}
+		
+		translate(in, out, overwrite, append);
+		t.stop("Time: \t");
+	}
+	
+	/** Translates VCF to GFF */
+	private static void translate(String in, String out, boolean overwrite, boolean append){
+		//Create output FileFormat objects
+		FileFormat ffout=FileFormat.testOutput(out, FileFormat.GFF, "gff", true, overwrite, append, false);
+
+		//Create input FileFormat objects
+		FileFormat ffin=FileFormat.testInput(in, FileFormat.VCF, "vcf", true, true);
+		
+		ByteFile bf=ByteFile.makeByteFile(ffin);
+		ByteStreamWriter bsw=null;
+		if(ffout!=null){
+			bsw=new ByteStreamWriter(ffout);
+			bsw.start();
+		}
+		
+		ByteBuilder bb=new ByteBuilder(17000);
+		bb.append("##gff-version 3\n");
+		String header="#seqid	source	type	start	end	score	strand	phase	attributes";
+		for(byte[] line=bf.nextLine(); line!=null; line=bf.nextLine()){
+			if(line.length>1){
+				if(line[0]=='#'){
+					if(Tools.startsWith(line, "##fileformat") || Tools.startsWith(line, "##FORMAT") || 
+							Tools.startsWith(line, "##INFO") || Tools.startsWith(line, "#CHROM	POS")){
+						//skip
+					}else{
+						int i=1;
+						while(i<line.length && line[i]=='#'){i++;}
+						i--;
+						bb.append(line, i, line.length-i);
+						bb.nl();
+					}
+				}else{
+					if(header!=null){
+						bb.append(header).append('\n');
+						header=null;
+					}
+					VCFLine vline=new VCFLine(line);
+					GffLine gline=new GffLine(vline);
+					gline.appendTo(bb);
+					bb.nl();
+				}
+			}
+			if(bb.length()>=16384){
+				if(bsw!=null){
+					bsw.print(bb);
+				}
+				bb.clear();
+			}
+		}
+		if(bb.length()>0){
+			if(bsw!=null){
+				bsw.print(bb);
+			}
+			bb.clear();
+		}
+		bf.close();
+		if(bsw!=null){bsw.poisonAndWait();}
+	}
+	
+}